2XS4 Hydrolase date Sep 24, 2010
title Structure Of Karilysin Catalytic Mmp Domain In Complex With
authors N.Cerda-Costa, T.Guevara, A.Y.Karim, M.Ksiazek, K.A.Nguyen, J.L. J.Potempa, F.X.Gomis-Ruth
compound source
Molecule: Karilysin Protease
Chain: A
Fragment: Residues 35-201
Synonym: Karilysin Catalytic Domain Kly18
Engineered: Yes
 Organism_scientific: Tannerella Forsythia
Organism_taxid: 28112
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

Molecule: Peptide Ala-Phe-Thr
Chain: B
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: I 4
R_factor 0.158 R_Free 0.186
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.790 85.790 53.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand CL, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases., Cerda-Costa N, Guevara T, Karim AY, Ksiazek M, Nguyen KA, Arolas JL, Potempa J, Gomis-Ruth FX, Mol Microbiol. 2011 Jan;79(1):119-132. doi:, 10.1111/j.1365-2958.2010.07434.x. Epub 2010 Nov 2. PMID:21166898
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (2xs4.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 2XS4
  • CSU: Contacts of Structural Units for 2XS4
  • Structure Factors (362 Kb)
  • Retrieve 2XS4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XS4 from S2C, [Save to disk]
  • Re-refined 2xs4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2XS4 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 2XS4
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2XS4, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xs4_B] [2xs4_A] [2xs4]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2XS4: [ZnMc ] by SMART
    • Other resources with information on 2XS4
  • Community annotation for 2XS4 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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